# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 08:53:30 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: trifluoro-[hydroxy-[hydroxy-[2-[(3-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@](=O)(OCCNc1cccc(c1)[N+]([O-])=O)O[P@@](O)(=O)O[Be-](F)(F)F
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 MNQ  MNQ  trifluoro-[hydroxy-[hydroxy-[2-[(3-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium  ligand  36  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNQ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 MNQ  BE    BE  BE    -1   0.733  33.0735  58.8648  23.3831
 MNQ  F1    F   F      0  -0.606  32.3112  58.3418  24.5495
 MNQ  F2    F   F      0  -0.574  32.1403  58.9056  22.0555
 MNQ  F3    F   F      0  -0.604  33.8714  60.1109  23.5270
 MNQ  PB    P   P      0   1.526  34.1280  56.7380  21.6986
 MNQ  OB1   O   O      0  -0.328  33.7590  55.2800  22.2397
 MNQ  OB2   O   OH1    0  -0.756  33.0906  57.2742  20.6942
 MNQ  OB3   O   OC2    0  -0.656  34.3011  57.5497  22.9506
 MNQ  OA3   O   O2     0  -0.677  35.4744  56.4749  20.8779
 MNQ  PA    P   P      0   1.487  36.1168  57.4949  19.7607
 MNQ  OA1   O   OH1    0  -0.706  35.5617  56.9504  18.3874
 MNQ  OA2   O   O      0  -0.670  35.8881  58.9028  20.1146
 MNQ  OE2   O   O2     0  -0.563  37.5935  56.9435  19.6871
 MNQ  NA3   N   NH1    0  -0.701  40.8303  56.7861  21.3406
 MNQ  CA2   C   CH2    0  -0.308  39.8751  56.6804  20.2664
 MNQ  CA1   C   CH2    0  -0.190  38.5137  57.1084  20.7760
 MNQ  C1    C   CR6    0   0.399  42.1429  56.4335  21.1714
 MNQ  C6    C   CR16   0  -0.317  43.0850  56.7844  22.1534
 MNQ  C5    C   CR16   0  -0.239  44.4103  56.4210  22.0307
 MNQ  C4    C   CR16   0  -0.314  44.8593  55.6942  20.9349
 MNQ  C3    C   CR6    0   0.283  43.9241  55.3561  19.9733
 MNQ  C2    C   CR16   0  -0.394  42.5848  55.7115  20.0599
 MNQ  N3    N   N      1   0.329  44.3610  54.5972  18.8069
 MNQ  O3A   O   O     -1  -0.380  43.5305  54.2721  17.9908
 MNQ  O3B   O   O      0  -0.379  45.5352  54.3270  18.7112
 MNQ  HOB2  H   HOH1   0   0.539  32.5340  58.0596  21.2155
 MNQ  HOA2  H   HOH1   0   0.516  34.9309  57.5349  17.9438
 MNQ  HNA1  H   HNH1   0   0.391  40.6859  57.5545  21.9779
 MNQ  HA21  H   HCH2   0   0.244  40.1550  57.2897  19.3976
 MNQ  HA22  H   HCH2   0   0.255  39.8106  55.6416  19.9335
 MNQ  HA11  H   HCH2   0   0.256  38.5308  58.1521  21.0991
 MNQ  HA12  H   HCH2   0   0.261  38.2095  56.4855  21.6196
 MNQ  H6    H   HCR6   0   0.278  42.7620  57.3474  23.0208
 MNQ  H5    H   HCR6   0   0.275  45.1125  56.7069  22.8021
 MNQ  H4    H   HCR6   0   0.289  45.8974  55.4122  20.8495
 MNQ  H2    H   HCR6   0   0.303  41.9009  55.4340  19.2720

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 MNQ  BE   F1    single    1.488  0.020  1.488
 MNQ  BE   F2    single    1.623  0.020  1.623
 MNQ  BE   F3    single    1.487  0.020  1.487
 MNQ  BE   OB3   single    1.850  0.020  1.850
 MNQ  PB   OB1   double    1.598  0.020  1.598
 MNQ  PB   OB2   single    1.540  0.020  1.540
 MNQ  PB   OB3   single    1.502  0.020  1.502
 MNQ  PB   OA3   single    1.599  0.020  1.599
 MNQ  OB2  HOB2  single    0.850  0.020  0.980
 MNQ  OA3  PA    single    1.643  0.020  1.643
 MNQ  PA   OA1   single    1.578  0.020  1.578
 MNQ  PA   OA2   double    1.470  0.020  1.470
 MNQ  PA   OE2   single    1.578  0.020  1.578
 MNQ  OA1  HOA2  single    0.850  0.020  0.980
 MNQ  OE2  CA1   single    1.435  0.020  1.435
 MNQ  NA3  CA2   single    1.441  0.020  1.441
 MNQ  NA3  C1    single    1.370  0.020  1.370
 MNQ  NA3  HNA1  single    0.890  0.020  1.040
 MNQ  CA2  CA1   single    1.515  0.020  1.515
 MNQ  CA2  HA21  single    0.970  0.020  1.090
 MNQ  CA2  HA22  single    0.970  0.020  1.090
 MNQ  CA1  HA11  single    0.970  0.020  1.090
 MNQ  CA1  HA12  single    0.970  0.020  1.090
 MNQ  C1   C6    aromatic  1.405  0.020  1.405
 MNQ  C1   C2    aromatic  1.397  0.020  1.397
 MNQ  C6   C5    aromatic  1.380  0.020  1.380
 MNQ  C6   H6    single    0.930  0.020  1.080
 MNQ  C5   C4    aromatic  1.389  0.020  1.389
 MNQ  C5   H5    single    0.930  0.020  1.080
 MNQ  C4   C3    aromatic  1.383  0.020  1.383
 MNQ  C4   H4    single    0.930  0.020  1.080
 MNQ  C3   C2    aromatic  1.388  0.020  1.388
 MNQ  C3   N3    single    1.459  0.020  1.459
 MNQ  C2   H2    single    0.930  0.020  1.080
 MNQ  N3   O3A   single    1.209  0.020  1.209
 MNQ  N3   O3B   double    1.209  0.020  1.209

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 MNQ  OB3   BE   F3    105.21  3.000
 MNQ  OB3   BE   F2    102.01  3.000
 MNQ  F3    BE   F2    111.51  3.000
 MNQ  OB3   BE   F1    105.85  3.000
 MNQ  F3    BE   F1    119.58  3.000
 MNQ  F2    BE   F1    110.81  3.000
 MNQ  OA3   PB   OB3   114.82  3.000
 MNQ  OA3   PB   OB2   106.84  3.000
 MNQ  OB3   PB   OB2   115.66  3.000
 MNQ  OA3   PB   OB1   102.60  3.000
 MNQ  OB3   PB   OB1   103.73  3.000
 MNQ  OB2   PB   OB1   112.51  3.000
 MNQ  HOB2  OB2  PB    106.36  3.000
 MNQ  PB    OB3  BE    120.17  3.000
 MNQ  PA    OA3  PB    125.17  3.000
 MNQ  OE2   PA   OA2   119.44  3.000
 MNQ  OE2   PA   OA1    99.67  3.000
 MNQ  OA2   PA   OA1   119.03  3.000
 MNQ  OE2   PA   OA3   100.41  3.000
 MNQ  OA2   PA   OA3   111.72  3.000
 MNQ  OA1   PA   OA3   103.88  3.000
 MNQ  HOA2  OA1  PA    114.82  3.000
 MNQ  CA1   OE2  PA    121.63  3.000
 MNQ  HNA1  NA3  C1    114.28  3.000
 MNQ  HNA1  NA3  CA2   115.59  3.000
 MNQ  C1    NA3  CA2   121.62  3.000
 MNQ  HA22  CA2  HA21  107.55  3.000
 MNQ  HA22  CA2  CA1   108.54  3.000
 MNQ  HA21  CA2  CA1   109.79  3.000
 MNQ  HA22  CA2  NA3   109.63  3.000
 MNQ  HA21  CA2  NA3   112.35  3.000
 MNQ  CA1   CA2  NA3   108.91  3.000
 MNQ  HA12  CA1  HA11  108.71  3.000
 MNQ  HA12  CA1  CA2   110.42  3.000
 MNQ  HA11  CA1  CA2   110.80  3.000
 MNQ  HA12  CA1  OE2   110.00  3.000
 MNQ  HA11  CA1  OE2   110.13  3.000
 MNQ  CA2   CA1  OE2   106.76  3.000
 MNQ  C2    C1   C6    118.22  3.000
 MNQ  C2    C1   NA3   122.30  3.000
 MNQ  C6    C1   NA3   119.47  3.000
 MNQ  H6    C6   C5    119.64  3.000
 MNQ  H6    C6   C1    119.29  3.000
 MNQ  C5    C6   C1    121.07  3.000
 MNQ  H5    C5   C4    119.40  3.000
 MNQ  H5    C5   C6    119.38  3.000
 MNQ  C4    C5   C6    121.22  3.000
 MNQ  H4    C4   C3    122.10  3.000
 MNQ  H4    C4   C5    120.66  3.000
 MNQ  C3    C4   C5    117.23  3.000
 MNQ  N3    C3   C2    118.17  3.000
 MNQ  N3    C3   C4    118.72  3.000
 MNQ  C2    C3   C4    123.11  3.000
 MNQ  H2    C2   C3    119.98  3.000
 MNQ  H2    C2   C1    120.87  3.000
 MNQ  C3    C2   C1    119.15  3.000
 MNQ  O3B   N3   O3A   123.63  3.000
 MNQ  O3B   N3   C3    118.08  3.000
 MNQ  O3A   N3   C3    118.29  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 MNQ  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 MNQ  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 MNQ  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 MNQ  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 MNQ  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 MNQ  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 MNQ  CONST_07  C5   C6   C1   NA3   180.00   0.0  0
 MNQ  CONST_08  C3   C2   C1   NA3   180.00   0.0  0
 MNQ  CONST_09  N3   C3   C2   C1    180.00   0.0  0
 MNQ  CONST_10  N3   C3   C4   C5    180.00   0.0  0
 MNQ  CONST_11  H5   C5   C6   C1    180.00   0.0  0
 MNQ  CONST_12  H2   C2   C1   C6    180.00   0.0  0
 MNQ  CONST_13  H4   C4   C5   C6    180.00   0.0  0
 MNQ  CONST_14  H6   C6   C5   C4    180.00   0.0  0
 MNQ  Var_01    C6   C1   NA3  CA2   168.10  30.0  2
 MNQ  Var_02    O3A  N3   C3   C4    177.87  30.0  2
 MNQ  Var_03    C1   NA3  CA2  CA1   178.55  30.0  3
 MNQ  Var_04    OB1  PB   OB3  BE   -110.69  30.0  3
 MNQ  Var_05    OA1  PA   OA3  PB    -94.99  30.0  3
 MNQ  Var_06    CA2  CA1  OE2  PA   -170.41  30.0  3
 MNQ  Var_07    NA3  CA2  CA1  OE2  -178.12  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 MNQ  chir_01  PB  OB2  OB3  OA3  both
 MNQ  chir_02  PA  OA1  OA2  OE2  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 MNQ  plan-1  NA3  0.020
 MNQ  plan-1  C1   0.020
 MNQ  plan-1  C6   0.020
 MNQ  plan-1  C5   0.020
 MNQ  plan-1  C4   0.020
 MNQ  plan-1  C3   0.020
 MNQ  plan-1  C2   0.020
 MNQ  plan-1  N3   0.020
 MNQ  plan-1  H6   0.020
 MNQ  plan-1  H5   0.020
 MNQ  plan-1  H4   0.020
 MNQ  plan-1  H2   0.020

